Bowtie2 - Align Reads to Long Reference Sequences

Bowtie 2 is an ultrafast and memory-efficient tool for
aligning sequencing reads to long reference sequences. It is
particularly good at aligning reads of about 50 up to 100s or
1,000s of characters to relatively long (e.g. mammalian)
genomes. Bowtie 2 indexes the genome with an FM Index (based
on the Burrows-Wheeler Transform or BWT) to keep its memory
footprint small: for the human genome, its memory footprint is
typically around 3.2 gigabytes of RAM. Bowtie 2 supports
gapped, local, and paired-end alignment modes. Multiple
processors can be used simultaneously to achieve greater
alignment speed.